PACT prevents aberrant activation of PKR by endogenous dsRNA without sequestration

Authors: Sadeem Ahmad, Tao Zou, Jihee Hwang, Linlin Zhao, Xi Wang, Anton Davydenko, Ilana Buchumenski, Patrick Zhuang, Alyssa R. Fishbein, Diego Capcha-Rodriguez, Aaron Orgel, Erez Y. Levanon, Sua Myong, James Chou, Matthew Meyerson, Sun Hur

Source: Nature Communications, Vol 16, Iss 1, Pp 1-17 (2025)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/4957ce693ea74404b36af8ebfdbe2888

Comprehensive mutational scanning of EGFR reveals TKI sensitivities of extracellular domain mutants

Authors: Tikvah K. Hayes, Elisa Aquilanti, Nicole S. Persky, Xiaoping Yang, Erica E. Kim, Lisa Brenan, Amy B. Goodale, Douglas Alan, Ted Sharpe, Robert E. Shue, Lindsay Westlake, Lior Golomb, Brianna R. Silverman, Myshal D. Morris, Ty Running Fisher, Eden Beyene, Yvonne Y. Li, Andrew D. Cherniack, Federica Piccioni, J. Kevin Hicks, Andrew S. Chi, Daniel P. Cahill, Jorg Dietrich, Tracy T. Batchelor, David E. Root, Cory M. Johannessen, Matthew Meyerson

Source: Nature Communications, Vol 15, Iss 1, Pp 1-18 (2024)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/0edde2f4b771457398e829246efe16d1

Comprehensive genomic characterization of HER2-low and HER2-0 breast cancer

Authors: Paolo Tarantino, Hersh Gupta, Melissa E. Hughes, Janet Files, Sarah Strauss, Gregory Kirkner, Anne-Marie Feeney, Yvonne Li, Ana C. Garrido-Castro, Romualdo Barroso-Sousa, Brittany L. Bychkovsky, Simona DiLascio, Lynette Sholl, Laura MacConaill, Neal Lindeman, Bruce E. Johnson, Matthew Meyerson, Rinath Jeselsohn, Xintao Qiu, Rong Li, Henry Long, Eric P. Winer, Deborah Dillon, Giuseppe Curigliano, Andrew D. Cherniack, Sara M. Tolaney, Nancy U. Lin

Source: Nature Communications, Vol 14, Iss 1, Pp 1-10 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/5c5258c1093e4d42ab2f76c5fe3ba511

XRN1 deletion induces PKR-dependent cell lethality in interferon-activated cancer cells

Authors: Tao Zou, Meng Zhou, Akansha Gupta, Patrick Zhuang, Alyssa R. Fishbein, Hope Y. Wei, Diego Capcha-Rodriguez, Zhouwei Zhang, Andrew D. Cherniack, Matthew Meyerson

Source: Cell Reports, Vol 43, Iss 2, Pp 113600- (2024)

Subject Terms: CP: Immunology, CP: Cancer, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124723016121; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/b352a4525a2640a6bc9eb5da3f7e76e9

Genomic insights into the mechanisms of FGFR1 dependency in squamous cell lung cancer

Authors: Netta Mäkinen, Matthew Meyerson

Source: The Journal of Clinical Investigation, Vol 133, Iss 21 (2023)

Subject Terms: Medicine

File Description: electronic resource

Relation: https://doaj.org/toc/1558-8238

Access URL: https://doaj.org/article/70cc8d34b272451993f8a03009192519

Author Correction: Comprehensive mutational scanning of EGFR reveals TKI sensitivities of extracellular domain mutants

Authors: Tikvah K. Hayes, Elisa Aquilanti, Nicole S. Persky, Xiaoping Yang, Erica E. Kim, Lisa Brenan, Amy B. Goodale, Douglas Alan, Ted Sharpe, Robert E. Shue, Lindsay Westlake, Lior Golomb, Brianna R. Silverman, Myshal D. Morris, Ty Running Fisher, Eden Beyene, Yvonne Y. Li, Andrew D. Cherniack, Federica Piccioni, J. Kevin Hicks, Andrew S. Chi, Daniel P. Cahill, Jorg Dietrich, Tracy T. Batchelor, David E. Root, Cory M. Johannessen, Matthew Meyerson

Source: Nature Communications, Vol 15, Iss 1, Pp 1-1 (2024)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/c60cde2e831e452ca04b334e2136cd27

Whole genome sequencing reveals the independent clonal origin of multifocal ileal neuroendocrine tumors

Authors: Netta Mäkinen, Meng Zhou, Zhouwei Zhang, Yosuke Kasai, Elizabeth Perez, Grace E. Kim, Chrissie Thirlwell, Eric Nakakura, Matthew Meyerson

Source: Genome Medicine, Vol 14, Iss 1, Pp 1-12 (2022)

Subject Terms: Small bowel, Small intestinal neuroendocrine tumors, Multifocality, Whole genome sequencing, Independent clonal origin, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/f9011e38723945a8b27005a687cbe565

Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres

Authors: Kar-Tong Tan, Michael K. Slevin, Matthew Meyerson, Heng Li

Source: Genome Biology, Vol 23, Iss 1, Pp 1-16 (2022)

Subject Terms: Nanopore-sequencing, Long-reads, Telomere, Basecalling, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/6921671e9266423d8abbf994a9c353f1

Author Correction: Comprehensive genomic characterization of HER2-low and HER2-0 breast cancer

Authors: Paolo Tarantino, Hersh Gupta, Melissa E. Hughes, Janet Files, Sarah Strauss, Gregory Kirkner, Anne-Marie Feeney, Yvonne Li, Ana C. Garrido-Castro, Romualdo Barroso-Sousa, Brittany L. Bychkovsky, Simona DiLascio, Lynette Sholl, Laura MacConaill, Neal Lindeman, Bruce E. Johnson, Matthew Meyerson, Rinath Jeselsohn, Xintao Qiu, Rong Li, Henry Long, Eric P. Winer, Deborah Dillon, Giuseppe Curigliano, Andrew D. Cherniack, Sara M. Tolaney, Nancy U. Lin

Source: Nature Communications, Vol 14, Iss 1, Pp 1-1 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/7fa2341e1b6d47c4bb97fd8b26758d3c

Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase

Authors: Colin W. Garvie, Xiaoyun Wu, Malvina Papanastasiou, Sooncheol Lee, James Fuller, Gavin R. Schnitzler, Steven W. Horner, Andrew Baker, Terry Zhang, James P. Mullahoo, Lindsay Westlake, Stephanie H. Hoyt, Marcus Toetzl, Matthew J. Ranaghan, Luc de Waal, Joseph McGaunn, Bethany Kaplan, Federica Piccioni, Xiaoping Yang, Martin Lange, Adrian Tersteegen, Donald Raymond, Timothy A. Lewis, Steven A. Carr, Andrew D. Cherniack, Christopher T. Lemke, Matthew Meyerson, Heidi Greulich

Source: Nature Communications, Vol 12, Iss 1, Pp 1-16 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/8c9d393dbd6b4b13a8ba16d21da8b36d

Haplotype-resolved germline and somatic alterations in renal medullary carcinomas

Authors: Kar-Tong Tan, Hyunji Kim, Jian Carrot-Zhang, Yuxiang Zhang, Won Jun Kim, Guillaume Kugener, Jeremiah A. Wala, Thomas P. Howard, Yueh-Yun Chi, Rameen Beroukhim, Heng Li, Gavin Ha, Seth L. Alper, Elizabeth J. Perlman, Elizabeth A. Mullen, William C. Hahn, Matthew Meyerson, Andrew L. Hong

Source: Genome Medicine, Vol 13, Iss 1, Pp 1-13 (2021)

Subject Terms: Linked-read sequencing, Haplotypes, Renal medullary carcinoma, Sickle cell trait, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/500d30bc4a054d33b395ec98271cf7b5

Analysis of germline-driven ancestry-associated gene expression in cancers

Authors: Nyasha Chambwe, Rosalyn W. Sayaman, Donglei Hu, Scott Huntsman, Anab Kemal, Samantha Caesar-Johnson, Jean C. Zenklusen, Elad Ziv, Rameen Beroukhim, Andrew D. Cherniack, Jian Carrot-Zhang, Ashton C. Berger, Seunghun Han, Matthew Meyerson, Jeffrey S. Damrauer, Katherine A. Hoadley, Ina Felau, John A. Demchok, Michael K.A. Mensah, Roy Tarnuzzer, Zhining Wang, Liming Yang, Theo A. Knijnenburg, A. Gordon Robertson, Christina Yau, Christopher Benz, Kuan-lin Huang, Justin Y. Newberg, Garrett M. Frampton, R. Jay Mashl, Li Ding, Alessandro Romanel, Francesca Demichelis, Wanding Zhou, Peter W. Laird, Hui Shen, Christopher K. Wong, Joshua M. Stuart, Alexander J. Lazar, Xiuning Le, Ninad Oak

Source: STAR Protocols, Vol 3, Iss 3, Pp 101586- (2022)

Subject Terms: Bioinformatics, Sequence analysis, Cancer, Genomics, RNAseq, Gene Expression, Science (General), Q1-390

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S266616672200466X; https://doaj.org/toc/2666-1667

Access URL: https://doaj.org/article/58eb09142b5d45b991b34126ef4e9377

Patterns of structural variation define prostate cancer across disease states

Authors: Meng Zhou, Minjeong Ko, Anna C.H. Hoge, Kelsey Luu, Yuzhen Liu, Magdalena L. Russell, William W. Hannon, Zhenwei Zhang, Jian Carrot-Zhang, Rameen Beroukhim, Eliezer M. Van Allen, Atish D. Choudhury, Peter S. Nelson, Matthew L. Freedman, Mary-Ellen Taplin, Matthew Meyerson, Srinivas R. Viswanathan, Gavin Ha

Source: JCI Insight, Vol 7, Iss 17 (2022)

Subject Terms: Genetics, Oncology, Medicine

File Description: electronic resource

Relation: https://doaj.org/toc/2379-3708

Access URL: https://doaj.org/article/6032eee655da4206a5a620a0aa119445

Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-2

Authors: Jason Nomburg, Matthew Meyerson, James A. DeCaprio

Source: Genome Medicine, Vol 12, Iss 1, Pp 1-14 (2020)

Subject Terms: SARS-CoV-2, COVID-19, Direct RNA sequencing, Transcription, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/c9f8efce104246e099617568dda9fcdd

Long-read sequencing reveals complex patterns of wraparound transcription in polyomaviruses.

Authors: Jason Nomburg, Wei Zou, Thomas C Frost, Chandreyee Datta, Shobha Vasudevan, Gabriel J Starrett, Michael J Imperiale, Matthew Meyerson, James A DeCaprio

Source: PLoS Pathogens, Vol 18, Iss 4, p e1010401 (2022)

Subject Terms: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1553-7366; https://doaj.org/toc/1553-7374

Access URL: https://doaj.org/article/617256a3a1db4dce84c7251edeb7863b

Analytical protocol to identify local ancestry-associated molecular features in cancer

Authors: Jian Carrot-Zhang, Seunghun Han, Wanding Zhou, Jeffrey S. Damrauer, Anab Kemal, Andrew D. Cherniack, Rameen Beroukhim, Ashton C. Berger, Matthew Meyerson, Katherine A. Hoadley, Ina Felau, Samantha Caesar-Johnson, John A. Demchok, Michael K.A. Mensah, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Nyasha Chambwe, Theo A. Knijnenburg, A. Gordon Robertson, Christina Yau, Christopher Benz, Kuan-lin Huang, Justin Newberg, Garret Frampton, R. Jay Mashl, Li Ding, Alessandro Romanel, Francesca Demichelis, Rosalyn W. Sayaman, Elad Ziv, Peter W. Laird, Hui Shen, Christopher K. Wong, Joshua M. Stuart, Alexander J. Lazar, Xiuning Le, Ninad Oak

Source: STAR Protocols, Vol 2, Iss 4, Pp 100766- (2021)

Subject Terms: Bioinformatics, Cancer, Genomics, Science (General), Q1-390

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S266616672100472X; https://doaj.org/toc/2666-1667

Access URL: https://doaj.org/article/57ccfed30daa47de8636a9bc5c03e2a0

Genomic and immune profiling of pre-invasive lung adenocarcinoma

Authors: Haiquan Chen, Jian Carrot-Zhang, Yue Zhao, Haichuan Hu, Samuel S. Freeman, Su Yu, Gavin Ha, Alison M. Taylor, Ashton C. Berger, Lindsay Westlake, Yuanting Zheng, Jiyang Zhang, Aruna Ramachandran, Qiang Zheng, Yunjian Pan, Difan Zheng, Shanbo Zheng, Chao Cheng, Muyu Kuang, Xiaoyan Zhou, Yang Zhang, Hang Li, Ting Ye, Yuan Ma, Zhendong Gao, Xiaoting Tao, Han Han, Jun Shang, Ying Yu, Ding Bao, Yechao Huang, Xiangnan Li, Yawei Zhang, Jiaqing Xiang, Yihua Sun, Yuan Li, Andrew D. Cherniack, Joshua D. Campbell, Leming Shi, Matthew Meyerson

Source: Nature Communications, Vol 10, Iss 1, Pp 1-6 (2019)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/4a9c53d05b3d4f2bb8b67fc34b59ad6c

Patient-derived lung cancer organoids as in vitro cancer models for therapeutic screening

Authors: Minsuh Kim, Hyemin Mun, Chang Oak Sung, Eun Jeong Cho, Hye-Joon Jeon, Sung-Min Chun, Da Jung Jung, Tae Hoon Shin, Gi Seok Jeong, Dong Kwan Kim, Eun Kyung Choi, Seong-Yun Jeong, Alison M. Taylor, Sejal Jain, Matthew Meyerson, Se Jin Jang

Source: Nature Communications, Vol 10, Iss 1, Pp 1-15 (2019)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/ce888df5d1284e7192c86d55942e13a0

Genomic Evolution in a Patient With Lung Adenocarcinoma With a Germline EGFR T790M Mutation

Authors: Netta Mäkinen, PhD, Meng Zhou, PhD, Meredith Bemus, BS, Julius Nevin, BS, Anwesha Nag, PhD, Ruthia Chen, BA, Yolonda L. Colson, MD, PhD, Aaron R. Thorner, PhD, Geoffrey R. Oxnard, MD, Matthew Meyerson, MD, PhD, Lynette M. Sholl, MD

Source: JTO Clinical and Research Reports, Vol 2, Iss 4, Pp 100146- (2021)

Subject Terms: NSCLC, Lung adenocarcinoma, EGFR germline mutation, High-throughput sequencing, Genome evolution, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666364321000059; https://doaj.org/toc/2666-3643

Access URL: https://doaj.org/article/f9832cdefc9b499baed9ecf7baf82cab

Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway

Authors: Jian Carrot-Zhang, Xiaotong Yao, Siddhartha Devarakonda, Aditya Deshpande, Jeffrey S. Damrauer, Tiago Chedraoui Silva, Christopher K. Wong, Hyo Young Choi, Ina Felau, A. Gordon Robertson, Mauro A.A. Castro, Lisui Bao, Esther Rheinbay, Eric Minwei Liu, Tuan Trieu, David Haan, Christina Yau, Toshinori Hinoue, Yuexin Liu, Ofer Shapira, Kiran Kumar, Karen L. Mungall, Hailei Zhang, Jake June-Koo Lee, Ashton Berger, Galen F. Gao, Binyamin Zhitomirsky, Wen-Wei Liang, Meng Zhou, Sitapriya Moorthi, Alice H. Berger, Eric A. Collisson, Michael C. Zody, Li Ding, Andrew D. Cherniack, Gad Getz, Olivier Elemento, Christopher C. Benz, Josh Stuart, J.C. Zenklusen, Rameen Beroukhim, Jason C. Chang, Joshua D. Campbell, D. Neil Hayes, Lixing Yang, Peter W. Laird, John N. Weinstein, David J. Kwiatkowski, Ming S. Tsao, William D. Travis, Ekta Khurana, Benjamin P. Berman, Katherine A. Hoadley, Nicolas Robine, Matthew Meyerson, Ramaswamy Govindan, Marcin Imielinski

Source: Cell Reports, Vol 34, Iss 8, Pp 108784- (2021)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124721000978; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/4264da604a8b4596a7e8b99d914ad26d